Improve tutorial1

.gitmodules

@@ -0,0 +1,8 @@
+[submodule ".dependencies/gromacstutorials-inputs"]
+	path = .dependencies/gromacstutorials-inputs
+	url = git@github.com:gromacstutorials/gromacstutorials-inputs.git
+	branch = main
+[submodule ".dependencies/pyplot-perso"]
+	path = .dependencies/pyplot-perso
+	url = git@github.com:simongravelle/pyplot-perso.git
+	branch = LAMMPS-livecom

docs/sphinx/compile.py

@@ -0,0 +1,53 @@
+import subprocess
+import re
+
+# Define ANSI escape codes for colors
+RED = '\033[91m'
+GREEN = '\033[92m'
+GRAY = '\033[90m'
+RESET = '\033[0m'
+
+def filter_make_output():
+
+    # Define multiple patterns to ignore
+    ignore_patterns = [
+        "Pygments lexer name 'bw' is not known",
+        "Pygments lexer name 'lammps' is not known",
+        ".. label:: start_",
+        ".. label:: end_",
+        "Unknown directive type"
+    ]
+
+    # Define a pattern to identify warnings (example pattern, adjust as needed)
+    warning_pattern = re.compile('|'.join(re.escape(p) for p in ["WARNING:", "ERROR:"]))
+
+    # Combine ignore patterns into a single regex pattern
+    ignore_pattern = re.compile('|'.join(re.escape(p) for p in ignore_patterns))
+
+    # Run 'make clean'
+    subprocess.run(['make', 'clean'], check=True)
+
+    # Run 'make html' and capture output
+    process = subprocess.Popen(['make', 'html'],
+                               stdout=subprocess.PIPE,
+                               stderr=subprocess.STDOUT, text=True)
+
+    # Read and filter output
+    output_lines = []
+    for line in process.stdout:
+        if len(line) > 1:
+            if not ignore_pattern.search(line):
+                # Determine the color based on whether the line matches the warning pattern
+                if warning_pattern.search(line):
+                    output_lines.append(RED + line + RESET)
+                else:
+                    output_lines.append(GRAY + line + RESET)
+
+    # Wait for the process to complete
+    process.wait()
+
+    # Print the filtered output
+    print(''.join(output_lines), end='')
+
+if __name__ == "__main__":
+    filter_make_output()

docs/sphinx/source/_static/custom.css

@@ -36,6 +36,26 @@
           mask-image: var(--icon--info);
 }
 
+/* New non-title information admonition */
+.admonition.non-title-info > .admonition-title {
+  display: none;  /* Hide the title */
+}
+
+.admonition.non-title-info {
+  background-color: #2962ff10;
+  border-color: #2963ff;
+  font-size: 13pt;
+}
+
+.admonition.non-title-info > .admonition-content {
+  color: #4b2d83;  /* Purple text color for contrast */
+}
+
+.admonition.non-title-info > .admonition-title::before {
+  content: '';  /* No icon needed, as there's no title */
+}
+
+
 :root { /*https://fontawesomeicons.com/svg/icons/info*/
   --icon--patreon: url('data:image/svg+xml;charset=utf-8,   <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"> <g> <path fill="none" d="M0 0h24v24H0z"/> <path d="M15 17a7.5 7.5 0 1 1 0-15 7.5 7.5 0 0 1 0 15zM2 2h4v20H2V2z"/> </g> </svg>')
 }